Genomics of multidrug-resistant Klebsiella pneumoniae isolates from community hospitals in Pretoria, South Africa.

OBJECTIVES

Multidrug-resistant (MDR) Klebsiella pneumoniae high-risk clones that produce carbapenemases and extended-spectrum β-lactamases (ESBLs) are a major public health threat, limiting treatment options. This study aimed to determine the prevalence, clonal diversity, and molecular characteristics of MDR carbapenemase-producing Klebsiella pneumoniae (CPKP) and ESBL-producing Klebsiella pneumoniae isolates from community hospitals in Pretoria, South Africa.

METHODS

Whole genome sequencing and polymerase chain reaction assays were used to characterize sequence types, resistance genes, and selected mobile genetic elements.

RESULTS

The bla OXA-48-like gene was the most detected carbapenemase gene, followed by bla NDM, bla KPC, and bla VIM. The prevalence of sequence type (ST) 307 was 34.7% (41 of 118) and 29.4% (10 of 34) in CPKP and ESBL-producing K. pneumoniae, respectively. Double-carbapenemase-producing K. pneumoniae clones included ST307 with bla NDM-1 + bla OXA-181, ST530 and ST2680 with bla KPC-2 + bla OXA-181, and pandrug-resistant ST2497 carrying bla NDM-1 + bla OXA-232. One ST17 isolate and one pandrug-resistant ST307 isolate harbored three carbapenemase genes (bla KPC + bla NDM + bla OXA-48-like).

CONCLUSION

The emergence and spread of new MDR K. pneumoniae high-risk clones with multiple carbapenemases in resource-constrained South African hospitals are a great concern due to limited treatment options. These findings call for urgent epidemiologic surveillance and enhanced infection prevention and control measures.